Why is the result of this GLSL shader asymetric when rendering with stereo "Side-By-Side"?
Moguri answered my question on the forums by posting this patch that fixes the Filter 2D issue in Blender.

The patch:

diff --git blender/source/gameengine/Rasterizer/RAS_2DFilterManager.cpp blender/source/gameengine/Rasterizer/RAS_2DFilterManager.cpp index 79ce853..1781852 100644
--- blender/source/gameengine/Rasterizer/RAS_2DFilterManager.cpp
+++ blender/source/gameengine/Rasterizer/RAS_2DFilterManager.cpp @@ -429,6 +429,9 @@ void RAS_2DFilterManager::RenderFilters(RAS_ICanvas* canvas)
        glActiveTextureARB(GL_TEXTURE0);
        canvas-&gt;SetViewPort(0, 0, rect_width-1, rect_height-1);  
+       RAS_Rect scissor_rect = canvas-&gt;GetDisplayArea();
+       glScissor(scissor_rect.GetLeft()+viewport[0], scissor_rect.GetBottom()+viewport[1], scissor_rect.GetWidth()+1, scissor_rect.GetHeight()+1);
+
        glDisable(GL_DEPTH_TEST);
        // in case the previous material was wire
        glPolygonMode(GL_FRONT_AND_BACK, GL_FILL);


Note: This patch is already included in the trunk, verified at 08/25/2013